[gmx-users] pull direction

[K.A. Feenstra]

Weihua Li wrote:
> Hi all,
>   Now i am confused about another problem.I will pull the 
> substrate along a certain channel.And i want to put the
> direction of the channel on z axis.But i don't know how to
> guarantee the direction of the channel to be the z axis.
> Below is my pull.ppa file.
[...]
>  i used the EDITCONF -rotate command to adjust the box
> direction.The channel direction looks to be at z axis.
> But how can i know the channel direction to exactly be z-axis?
>  Could anyone give me some advice?

You need to define an axis (a line) through your channel
in some way. you could for example use g_bundle and define
two groups of atoms, each around either end of the channel
(i.e. one group at the beginning and the other at the end).
Then you can seen whether this line runs parallel to the
Z-axis. You should also realise that your protein can
rotate during the simulation. Molecule rotation can be
removed, but I don't remember exactly how the options
work (check the online docs, the FAQ, or the list archive).


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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